chr17-65415739-C-T

Variant names:

• chr17-65415739-C-T
• rs4630583
• ENST00000778872.1:n.453-14461G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000778872.1(ENSG00000301434):​n.453-14461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,830 control chromosomes in the GnomAD database, including 40,637 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (40637 hom., cov: 30)
• Consequence: ENSG00000301434 ENST00000778872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

Genes affected

ENSG00000301434 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301434	ENST00000778872.1	n.453-14461G>A		intron_variant	Intron 1 of 1
ENSG00000301434	ENST00000778873.1	n.31-14461G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103099 AN: 151712 Hom.: 40634 Cov.: 30

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.679 AC: 103107 AN: 151830 Hom.: 40637 Cov.: 30 AF XY: 0.685 AC XY: 50817 AN XY: 74200

African (AFR) AF: 0.247 AC: 10221 AN: 41332

American (AMR) AF: 0.827 AC: 12632 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3033 AN: 3468

East Asian (EAS) AF: 0.583 AC: 2989 AN: 5124

South Asian (SAS) AF: 0.848 AC: 4072 AN: 4802

European-Finnish (FIN) AF: 0.853 AC: 9005 AN: 10560

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.863 AC: 58663 AN: 67960

Other (OTH) AF: 0.738 AC: 1553 AN: 2104

Alfa AF: 0.744 Hom.: 8016

Bravo AF: 0.656

Asia WGS AF: 0.664 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.25
DANN	Benign	0.92
PhyloP100		-0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4630583; hg19: chr17-63411857;